rs10809811

Variant names:

• chr9-12650996-C-G
• rs10809811
• ENST00000803542.1:n.310-19389G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000803542.1(LURAP1L-AS1):​n.310-19389G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,944 control chromosomes in the GnomAD database, including 18,542 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (18542 hom., cov: 31)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 4 publications found

Genes affected

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LURAP1L-AS1	ENST00000803542.1	n.310-19389G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66507 AN: 151824 Hom.: 18545 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.441

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.438 AC: 66521 AN: 151944 Hom.: 18542 Cov.: 31 AF XY: 0.432 AC XY: 32108 AN XY: 74270

African (AFR) AF: 0.157 AC: 6521 AN: 41472

American (AMR) AF: 0.342 AC: 5211 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4820

European-Finnish (FIN) AF: 0.690 AC: 7268 AN: 10532

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43013 AN: 67918

Other (OTH) AF: 0.438 AC: 923 AN: 2108

Alfa AF: 0.534 Hom.: 3037

Bravo AF: 0.400

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.47
DANN	Benign	0.78
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10809811; hg19: chr9-12650996;